In Indonesia, land use change (LUC) in the form of peatland degradation induces carbon loss through direct CO2 emissions, but also via soil leaching of which circa 50% is decomposed and emitted as CO2 from the rivers. However, the fate of the remaining exported leached carbon is uncertain. Here, we show that the majority of this carbon is respired in the estuaries and emitted to the atmosphere. However, a portion is adsorbed into the marine carbon pool where it favors CaCO3 dissolution and can therefore be seen as the invisible carbon footprint. We conclude that the effects of LUC stretch beyond the terrestrial realm and are not limited to CO2 emissions, but also affect marine ecosystems. Considering the ecological and economical importance of these ecosystems, it is important that this so far invisible carbon footprint, as well as the aquatic and marine CO2 emissions, are included in climate mitigation strategies.